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  <div class="section" id="gammasurface">
<h1>GammaSurface<a class="headerlink" href="#gammasurface" title="Permalink to this headline">¶</a></h1>
<dl class="class">
<dt id="atomman.defect.GammaSurface">
<em class="property">class </em><code class="sig-prename descclassname">atomman.defect.</code><code class="sig-name descname">GammaSurface</code><span class="sig-paren">(</span><em class="sig-param">model=None</em>, <em class="sig-param">a1vect=None</em>, <em class="sig-param">a2vect=None</em>, <em class="sig-param">a1=None</em>, <em class="sig-param">a2=None</em>, <em class="sig-param">E_gsf=None</em>, <em class="sig-param">box=None</em>, <em class="sig-param">delta=None</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.defect.GammaSurface" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.9)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
<p>Class for representing gamma surfaces, i.e., generalized stacking faults.</p>
<dl class="method">
<dt id="atomman.defect.GammaSurface.E_gsf">
<code class="sig-name descname">E_gsf</code><span class="sig-paren">(</span><em class="sig-param">**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.defect.GammaSurface.E_gsf" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns values for generalized stacking fault energy interpolated from
the raw data.  Values can be obtained relative to a1, a2 fractional
coordinates, x, y plotting coordinates, or pos Cartesian coordinates.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>a1</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>(</em><em>s</em><em>)</em><em>, </em><em>optional</em>) – Fractional coordinate(s) along a1vect.</p></li>
<li><p><strong>a2</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>(</em><em>s</em><em>)</em><em>, </em><em>optional</em>) – Fractional coordinate(s) along a2vect.</p></li>
<li><p><strong>pos</strong> (<em>np.array</em><em>, </em><em>optional</em>) – 3D Cartesian position vector(s).</p></li>
<li><p><strong>x</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>(</em><em>s</em><em>)</em><em>, </em><em>optional</em>) – Plotting x coordinate(s).</p></li>
<li><p><strong>y</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>(</em><em>s</em><em>)</em><em>, </em><em>optional</em>) – Plotting y coordinate(s).</p></li>
<li><p><strong>a1vect</strong> (<em>np.array</em><em>, </em><em>optional</em>) – Vector for the a1 fractional coordinates.  Default value of None
uses the saved a1vect.</p></li>
<li><p><strong>a2vect</strong> (<em>np.array</em><em>, </em><em>optional</em>) – Vector for the a2 fractional coordinates.  Default value of None
uses the saved a2vect.</p></li>
<li><p><strong>xvect</strong> (<em>np.array</em><em>, </em><em>optional</em>) – Cartesian vector corresponding to the plotting x-axis. If None
(default), this is taken as the Cartesian of a1vect.</p></li>
<li><p><strong>smooth</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – If True (default) the returned values are smoothed using a RBF fit.
If False, the closest measured values are returned.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.GammaSurface.E_gsf_line_plot">
<code class="sig-name descname">E_gsf_line_plot</code><span class="sig-paren">(</span><em class="sig-param">vect=None</em>, <em class="sig-param">num=None</em>, <em class="sig-param">smooth=True</em>, <em class="sig-param">length_unit='Å'</em>, <em class="sig-param">energyperarea_unit='eV/Å^2'</em>, <em class="sig-param">figsize=None</em>, <em class="sig-param">fig=None</em>, <em class="sig-param">**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.defect.GammaSurface.E_gsf_line_plot" title="Permalink to this definition">¶</a></dt>
<dd><p>Generates a line plot for the interpolated generalized stacking fault
energy along a specified crystallographic vector in the (a1, a2) plane.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>vect</strong> (<em>numpy.array</em><em>, </em><em>optional</em>) – Vector to plot the gsf along.  If box is set, this vect will be a
lattice vector, otherwise it will be a Cartesian vector.  Must be
in the plane defined by the GammaSurface object’s a1vect and
a2vect vectors.  Default value will use the set a1vect.</p></li>
<li><p><strong>num</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.9)"><em>int</em></a><em>, </em><em>optional</em>) – The number of points to evaluate the generalized stacking fault
energy for.  Default value is 100 if smooth is True, otherwise is
number of unique a1 values from 0 to 1.</p></li>
<li><p><strong>smooth</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – If True (default), then plot shows smooth interpolated values.
If False, plot shows nearest raw data values.</p></li>
<li><p><strong>length_unit</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – The unit of length to display the x-axis coordinates in.
Default value is ‘Å’.</p></li>
<li><p><strong>energyperarea_unit</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – The unit of energy per area to display the stacking fault energies
in. Default value is ‘eV/Å^2’.</p></li>
<li><p><strong>figsize</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.9)"><em>tuple</em></a><em>, </em><em>optional</em>) – The x,y size of the figure to return.  Default value is (10, 6).</p></li>
<li><p><strong>fig</strong> (<em>matplotlib.figure</em><em>, </em><em>optional</em>) – An existing figure object to add the new plot to.  If not given, a
new figure is generated.</p></li>
<li><p><strong>**kwargs</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.9)"><em>dict</em></a><em>, </em><em>optional</em>) – Additional keywords are passed into the underlying
matplotlib.pyplot.plot(). This allows control of such things
like line color, style, etc.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p></p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>matplotlib.figure</p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.GammaSurface.E_gsf_surface_plot">
<code class="sig-name descname">E_gsf_surface_plot</code><span class="sig-paren">(</span><em class="sig-param">normalize=False</em>, <em class="sig-param">smooth=True</em>, <em class="sig-param">a1vect=None</em>, <em class="sig-param">a2vect=None</em>, <em class="sig-param">xvect=None</em>, <em class="sig-param">length_unit='Å'</em>, <em class="sig-param">energyperarea_unit='eV/Å^2'</em>, <em class="sig-param">numx=100</em>, <em class="sig-param">numy=100</em>, <em class="sig-param">figsize=None</em>, <em class="sig-param">**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.defect.GammaSurface.E_gsf_surface_plot" title="Permalink to this definition">¶</a></dt>
<dd><p>Creates a 2D surface plot from the stacking fault energy values.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>normalize</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – Flag indicating if axes are Cartesian (False, default) or
normalized by a1, a2 vectors (True).</p></li>
<li><p><strong>smooth</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – If True (default), then plot shows smooth interpolated values.
If False, plot shows nearest raw data values.</p></li>
<li><p><strong>a1vect</strong> (<em>np.array</em><em>, </em><em>optional</em>) – Crystal vector for the a1 vector to use for plotting.  Default
value of None uses the saved a1vect.</p></li>
<li><p><strong>a2vect</strong> (<em>np.array</em><em>, </em><em>optional</em>) – Crystal vector for the a2 vector to use for plotting.  Default
value of None uses the saved a2vect.</p></li>
<li><p><strong>xvect</strong> (<em>numpy.array</em><em>, </em><em>optional</em>) – Crystal vector to align with the plotting x-axis for
non-normalized plots.  If not given, this is taken as the Cartesian
of a1vect.</p></li>
<li><p><strong>length_unit</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – The unit of length to display non-normalized axes values in.
Default value is ‘Å’.</p></li>
<li><p><strong>energyperarea_unit</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – The unit of energy per area to display the stacking fault energies
in. Default value is ‘eV/Å^2’.</p></li>
<li><p><strong>numx</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.9)"><em>int</em></a><em>, </em><em>optional</em>) – The number of plotting points to use along the x-axis.  Default
value is 100.</p></li>
<li><p><strong>numy</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.9)"><em>int</em></a><em>, </em><em>optional</em>) – The number of plotting points to use along the y-axis.  Default
value is 100.</p></li>
<li><p><strong>figsize</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.9)"><em>tuple</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.9)"><em>None</em></a><em>, </em><em>optional</em>) – The figure’s x,y dimensions.  If None (default), the values are
scaled such that the x,y spacings are approximately equal, and the
larger of the two values is set to 10.</p></li>
<li><p><strong>**kwargs</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.9)"><em>dict</em></a><em>, </em><em>optional</em>) – Additional keywords are passed into the underlying
matplotlib.pyplot.pcolormesh(). This allows control of such things
like the colormap (cmap).</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p></p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>matplotlib.figure</p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.GammaSurface.a12_to_pos">
<code class="sig-name descname">a12_to_pos</code><span class="sig-paren">(</span><em class="sig-param">a1</em>, <em class="sig-param">a2</em>, <em class="sig-param">a1vect=None</em>, <em class="sig-param">a2vect=None</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.defect.GammaSurface.a12_to_pos" title="Permalink to this definition">¶</a></dt>
<dd><p>Conversion function from normalized a1, a2 coordinates to Cartesian
positions.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>a1</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>(</em><em>s</em><em>)</em>) – Fractional distance(s) along a1 vector.</p></li>
<li><p><strong>a2</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>(</em><em>s</em><em>)</em>) – Fractional distance(s) along a2 vector.</p></li>
<li><p><strong>a1vect</strong> (<em>np.array</em><em>, </em><em>optional</em>) – Crystal vector for the a1 vector.  Default value of None uses the
saved a1vect.</p></li>
<li><p><strong>a2vect</strong> (<em>np.array</em><em>, </em><em>optional</em>) – Crystal vector for the a2 vector.  Default value of None uses the
saved a2vect.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>3D Cartesian position vector(s).</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>np.array</p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.GammaSurface.a12_to_xy">
<code class="sig-name descname">a12_to_xy</code><span class="sig-paren">(</span><em class="sig-param">a1</em>, <em class="sig-param">a2</em>, <em class="sig-param">a1vect=None</em>, <em class="sig-param">a2vect=None</em>, <em class="sig-param">xvect=None</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.defect.GammaSurface.a12_to_xy" title="Permalink to this definition">¶</a></dt>
<dd><p>Conversion function from normalized a1, a2 coordinates to plotting x, y
coordinates.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>a1</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>(</em><em>s</em><em>)</em>) – Fractional distance(s) along a1 vector.</p></li>
<li><p><strong>a2</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>(</em><em>s</em><em>)</em>) – Fractional distance(s) along a2 vector.</p></li>
<li><p><strong>a1vect</strong> (<em>np.array</em><em>, </em><em>optional</em>) – Crystal vector for the a1 vector.  Default value of None uses the
saved a1vect.</p></li>
<li><p><strong>a2vect</strong> (<em>np.array</em><em>, </em><em>optional</em>) – Crystal vector for the a2 vector.  Default value of None uses the
saved a2vect.</p></li>
<li><p><strong>xvect</strong> (<em>np.array</em><em>, </em><em>optional</em>) – Cartesian vector corresponding to the plotting x-axis. If None (default), this is
taken as the Cartesian of a1vect.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><ul class="simple">
<li><p><strong>x</strong> (<em>float(s)</em>) – Plotting x coordinate(s).</p></li>
<li><p><strong>y</strong> (<em>float(s)</em>) – Plotting y coordinate(s).</p></li>
</ul>
</p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.GammaSurface.a1vect">
<em class="property">property </em><code class="sig-name descname">a1vect</code><a class="headerlink" href="#atomman.defect.GammaSurface.a1vect" title="Permalink to this definition">¶</a></dt>
<dd><p>The a1 shifting vector.</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p>numpy.ndarray</p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.GammaSurface.a2vect">
<em class="property">property </em><code class="sig-name descname">a2vect</code><a class="headerlink" href="#atomman.defect.GammaSurface.a2vect" title="Permalink to this definition">¶</a></dt>
<dd><p>The a2 shifting vector.</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p>numpy.ndarray</p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.GammaSurface.box">
<em class="property">property </em><code class="sig-name descname">box</code><a class="headerlink" href="#atomman.defect.GammaSurface.box" title="Permalink to this definition">¶</a></dt>
<dd><p>A unit cell box used for converting between
crystal lattice and Cartesian vectors.</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p><a class="reference internal" href="atomman.Box.html#atomman.Box" title="atomman.Box">atomman.Box</a></p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.GammaSurface.build_path">
<code class="sig-name descname">build_path</code><span class="sig-paren">(</span><em class="sig-param">pos</em>, <em class="sig-param">npoints=31</em>, <em class="sig-param">style='ISM'</em>, <em class="sig-param">gradientfxn='cdiff'</em>, <em class="sig-param">gradientkwargs=None</em>, <em class="sig-param">integratorfxn='rk'</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.defect.GammaSurface.build_path" title="Permalink to this definition">¶</a></dt>
<dd><p>Builds a subclass of atomman.mep.BasePath as one or two line segments
along a gamma surface. The energy function along the path will be
properly set using E_gsf.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>pos</strong> (<em>array-like object</em>) – 2x3 or 3x3 array of Miller vector points that defines the end points of the path’s
line segment(s).</p></li>
<li><p><strong>npoints</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.9)"><em>int</em></a><em>, </em><em>optional</em>) – The number of points to include along the path. Must be odd if three pos are used.
Default value is 31.</p></li>
<li><p><strong>style</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a>) – The path/relaxer style to use.  Default value of ‘ISM’ will use improved string method.</p></li>
<li><p><strong>gradientfxn</strong> (<em>function</em><em>, </em><em>optional</em>) – The function to use to estimate the gradient of the energy.  Default
value of ‘cdiff’ will use atomman.mep.gradient.central_difference</p></li>
<li><p><strong>gradientkwargs</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.9)"><em>dict</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.9)"><em>None</em></a><em>, </em><em>optional</em>) – The keyword arguments (i.e. settings) to use with the gradientfxn.
Default value of None will use {‘shift’:1e-7}.</p></li>
<li><p><strong>integratorfxn</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><em>function</em><em>, </em><em>optional</em>) – The function to use to integrate relaxation steps.  Default value of
‘rk’ will use atomman.mep.integrator.rungekutta.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>Specific class dictated by style: style==’ISM’ -&gt; ISMPath (only style currently).</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>subclass of atomman.mep.BasePath</p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.GammaSurface.data">
<em class="property">property </em><code class="sig-name descname">data</code><a class="headerlink" href="#atomman.defect.GammaSurface.data" title="Permalink to this definition">¶</a></dt>
<dd><p>The raw data.</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p>pandas.DataFrame</p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.GammaSurface.delta">
<code class="sig-name descname">delta</code><span class="sig-paren">(</span><em class="sig-param">**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.defect.GammaSurface.delta" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns values for generalized stacking fault energy interpolated from
the raw data.  Values can be obtained relative to a1, a2 fractional
coordinates, x, y plotting coordinates, or pos Cartesian coordinates.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>a1</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>(</em><em>s</em><em>)</em><em>, </em><em>optional</em>) – Fractional coordinate(s) along a1vect.</p></li>
<li><p><strong>a2</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>(</em><em>s</em><em>)</em><em>, </em><em>optional</em>) – Fractional coordinate(s) along a2vect.</p></li>
<li><p><strong>pos</strong> (<em>np.array</em><em>, </em><em>optional</em>) – 3D Cartesian position vector(s).</p></li>
<li><p><strong>x</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>(</em><em>s</em><em>)</em><em>, </em><em>optional</em>) – Plotting x coordinate(s).</p></li>
<li><p><strong>y</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>(</em><em>s</em><em>)</em><em>, </em><em>optional</em>) – Plotting y coordinate(s).</p></li>
<li><p><strong>a1vect</strong> (<em>np.array</em><em>, </em><em>optional</em>) – Vector for the a1 fractional coordinates.  Default value of None
uses the saved a1vect.</p></li>
<li><p><strong>a2vect</strong> (<em>np.array</em><em>, </em><em>optional</em>) – Vector for the a2 fractional coordinates.  Default value of None
uses the saved a2vect.</p></li>
<li><p><strong>xvect</strong> (<em>np.array</em><em>, </em><em>optional</em>) – Cartesian vector corresponding to the plotting x-axis. If None
(default), this is taken as the Cartesian of a1vect.</p></li>
<li><p><strong>smooth</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – If True (default) the returned values are smoothed using a RBF fit.
If False, the closest measured values are returned.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.GammaSurface.delta_line_plot">
<code class="sig-name descname">delta_line_plot</code><span class="sig-paren">(</span><em class="sig-param">vect=None</em>, <em class="sig-param">num=None</em>, <em class="sig-param">smooth=True</em>, <em class="sig-param">length_unit='Å'</em>, <em class="sig-param">figsize=None</em>, <em class="sig-param">fig=None</em>, <em class="sig-param">**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.defect.GammaSurface.delta_line_plot" title="Permalink to this definition">¶</a></dt>
<dd><p>Generates a line plot for the interpolated delta planar shift values
along a specified crystallographic vector in the (a1, a2) plane.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>vect</strong> (<em>numpy.array</em><em>, </em><em>optional</em>) – Vector to plot the gsf along.  If box is set, this vect will be a
lattice vector, otherwise it will be a Cartesian vector.  Must be
in the plane defined by the GammaSurface object’s a1vect and
a2vect vectors.  Default value will use the set a1vect.</p></li>
<li><p><strong>num</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.9)"><em>int</em></a><em>, </em><em>optional</em>) – The number of points to evaluate the generalized stacking fault
energy for.  Default value is 100 if smooth is True, otherwise is
number of unique a1 values from 0 to 1.</p></li>
<li><p><strong>smooth</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – If True (default), then plot shows smooth interpolated values.
If False, plot shows nearest raw data values.</p></li>
<li><p><strong>length_unit</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – The unit of length to display the x-axis coordinates in.
Default value is ‘Å’.</p></li>
<li><p><strong>figsize</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.9)"><em>tuple</em></a><em>, </em><em>optional</em>) – The x,y size of the figure to return.  Default value is (10, 6).</p></li>
<li><p><strong>fig</strong> (<em>matplotlib.figure</em><em>, </em><em>optional</em>) – An existing figure object to add the new plot to.  If not given, a
new figure is generated.</p></li>
<li><p><strong>**kwargs</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.9)"><em>dict</em></a><em>, </em><em>optional</em>) – Additional keywords are passed into the underlying
matplotlib.pyplot.plot(). This allows control of such things
like line color, style, etc.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p></p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>matplotlib.figure</p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.GammaSurface.delta_surface_plot">
<code class="sig-name descname">delta_surface_plot</code><span class="sig-paren">(</span><em class="sig-param">normalize=False</em>, <em class="sig-param">smooth=True</em>, <em class="sig-param">a1vect=None</em>, <em class="sig-param">a2vect=None</em>, <em class="sig-param">xvect=None</em>, <em class="sig-param">length_unit='Å'</em>, <em class="sig-param">numx=100</em>, <em class="sig-param">numy=100</em>, <em class="sig-param">figsize=None</em>, <em class="sig-param">**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.defect.GammaSurface.delta_surface_plot" title="Permalink to this definition">¶</a></dt>
<dd><p>Creates a 2D surface plot from the delta planar displacement values.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>normalize</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – Flag indicating if axes are Cartesian (False, default) or
normalized by a1, a2 vectors (True).</p></li>
<li><p><strong>smooth</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – If True (default), then plot shows smooth interpolated values.
If False, plot shows nearest raw data values.</p></li>
<li><p><strong>a1vect</strong> (<em>np.array</em><em>, </em><em>optional</em>) – Crystal vector for the a1 vector to use for plotting.  Default
value of None uses the saved a1vect.</p></li>
<li><p><strong>a2vect</strong> (<em>np.array</em><em>, </em><em>optional</em>) – Crystal vector for the a2 vector to use for plotting.  Default
value of None uses the saved a2vect.</p></li>
<li><p><strong>xvect</strong> (<em>numpy.array</em><em>, </em><em>optional</em>) – Crystal vector to align with the plotting x-axis for
non-normalized plots.  If not given, this is taken as the Cartesian
of a1vect.</p></li>
<li><p><strong>length_unit</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – The unit of length to display delta and non-normalized axes values
in.  Default value is ‘Å’.</p></li>
<li><p><strong>numx</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.9)"><em>int</em></a><em>, </em><em>optional</em>) – The number of plotting points to use along the x-axis.  Default
value is 100.</p></li>
<li><p><strong>numy</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.9)"><em>int</em></a><em>, </em><em>optional</em>) – The number of plotting points to use along the y-axis.  Default
value is 100.</p></li>
<li><p><strong>figsize</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.9)"><em>tuple</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.9)"><em>None</em></a><em>, </em><em>optional</em>) – The figure’s x,y dimensions.  If None (default), the values are
scaled such that the x,y spacings are approximately equal, and the
larger of the two values is set to 10.</p></li>
<li><p><strong>**kwargs</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.9)"><em>dict</em></a><em>, </em><em>optional</em>) – Additional keywords are passed into the underlying
matplotlib.pyplot.pcolormesh(). This allows control of such things
like the colormap (cmap).</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p></p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>matplotlib.figure</p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.GammaSurface.fit">
<code class="sig-name descname">fit</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#atomman.defect.GammaSurface.fit" title="Permalink to this definition">¶</a></dt>
<dd><p>Defines the interpolation functions from the raw data.</p>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.GammaSurface.model">
<code class="sig-name descname">model</code><span class="sig-paren">(</span><em class="sig-param">model=None</em>, <em class="sig-param">length_unit='angstrom'</em>, <em class="sig-param">energyperarea_unit='mJ/m^2'</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.defect.GammaSurface.model" title="Permalink to this definition">¶</a></dt>
<dd><p>Return or set DataModelDict representation of the gamma surface.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>model</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>file-like object</em><em> or </em><em>DataModelDict</em><em>, </em><em>optional</em>) – XML/JSON content to extract gamma surface energy from. If not
given, model content will be generated.</p></li>
<li><p><strong>length_unit</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – Units to report delta displacement values in when a new model is
generated. Default value is ‘angstrom’.</p></li>
<li><p><strong>energyperarea_unit</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – Units to report fault energy values in when a new model is
generated.  Default value is ‘mJ/m^2’.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>A dictionary containing the stacking fault data of the
GammaSurface object.  Returned if model is not given.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>DataModelDict</p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.GammaSurface.path">
<code class="sig-name descname">path</code><span class="sig-paren">(</span><em class="sig-param">coord</em>, <em class="sig-param">style='ISM'</em>, <em class="sig-param">gradientfxn='cdiff'</em>, <em class="sig-param">gradientkwargs=None</em>, <em class="sig-param">integratorfxn='rk'</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.defect.GammaSurface.path" title="Permalink to this definition">¶</a></dt>
<dd><p>Creates an mep Path object mapping for the gamma surface based on
supplied xy coordinates along the path line.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>coord</strong> (<em>array-like object</em>) – The xy coordinates of the points along the path.</p></li>
<li><p><strong>style</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a>) – The path/relaxer style to use.  Default value of ‘ISM’ will use improved string method.</p></li>
<li><p><strong>gradientfxn</strong> (<em>function</em><em>, </em><em>optional</em>) – The function to use to estimate the gradient of the energy.  Default
value of ‘cdiff’ will use atomman.mep.gradient.central_difference</p></li>
<li><p><strong>gradientkwargs</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.9)"><em>dict</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.9)"><em>None</em></a><em>, </em><em>optional</em>) – The keyword arguments (i.e. settings) to use with the gradientfxn.
Default value of None will use {‘shift’:1e-7}.</p></li>
<li><p><strong>integratorfxn</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><em>function</em><em>, </em><em>optional</em>) – The function to use to integrate relaxation steps.  Default value of
‘rk’ will use atomman.mep.integrator.rungekutta.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>Specific class dictated by style: style==’ISM’ -&gt; ISMPath (only style currently).</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>subclass of atomman.mep.BasePath</p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.GammaSurface.planenormal">
<em class="property">property </em><code class="sig-name descname">planenormal</code><a class="headerlink" href="#atomman.defect.GammaSurface.planenormal" title="Permalink to this definition">¶</a></dt>
<dd><p>The Cartesian vector normal to the fault plane.</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p>numpy.ndarray</p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.GammaSurface.pos_to_a12">
<code class="sig-name descname">pos_to_a12</code><span class="sig-paren">(</span><em class="sig-param">pos</em>, <em class="sig-param">a1vect=None</em>, <em class="sig-param">a2vect=None</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.defect.GammaSurface.pos_to_a12" title="Permalink to this definition">¶</a></dt>
<dd><p>Conversion function from Cartesian positions to normalized a1, a2
coordinates.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>pos</strong> (<em>np.array</em>) – 3D Cartesian position vector(s).</p></li>
<li><p><strong>a1vect</strong> (<em>np.array</em><em>, </em><em>optional</em>) – Crystal vector for the a1 vector.  Default value of None uses the
saved a1vect.</p></li>
<li><p><strong>a2vect</strong> (<em>np.array</em><em>, </em><em>optional</em>) – Crystal vector for the a2 vector.  Default value of None uses the
saved a2vect.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><ul class="simple">
<li><p><strong>a1</strong> (<em>float(s)</em>) – Fractional distance(s) along a1 vector.</p></li>
<li><p><strong>a2</strong> (<em>float(s)</em>) – Fractional distance(s) along a2 vector.</p></li>
</ul>
</p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.GammaSurface.pos_to_xy">
<code class="sig-name descname">pos_to_xy</code><span class="sig-paren">(</span><em class="sig-param">pos</em>, <em class="sig-param">xvect=None</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.defect.GammaSurface.pos_to_xy" title="Permalink to this definition">¶</a></dt>
<dd><p>Conversion function from Cartesian positions to plotting x, y
coordinates.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>pos</strong> (<em>np.array</em>) – 3D Cartesian position vector(s).</p></li>
<li><p><strong>xvect</strong> (<em>np.array</em><em>, </em><em>optional</em>) – Cartesian vector corresponding to the plotting x-axis. If None (default), this is
taken as the Cartesian of a1vect.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><ul class="simple">
<li><p><strong>x</strong> (<em>float(s)</em>) – Plotting x coordinate(s).</p></li>
<li><p><strong>y</strong> (<em>float(s)</em>) – Plotting y coordinate(s).</p></li>
</ul>
</p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.GammaSurface.set">
<code class="sig-name descname">set</code><span class="sig-paren">(</span><em class="sig-param">a1vect</em>, <em class="sig-param">a2vect</em>, <em class="sig-param">a1</em>, <em class="sig-param">a2</em>, <em class="sig-param">E_gsf</em>, <em class="sig-param">box=None</em>, <em class="sig-param">delta=None</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.defect.GammaSurface.set" title="Permalink to this definition">¶</a></dt>
<dd><p>Sets generalized stacking fault data.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>a1vect</strong> (<em>array-like object</em>) – The a1 shifting vector.  If box is given, a1vect is taken as a
crystal lattice vector, otherwise as a Cartesian vector.</p></li>
<li><p><strong>a2vect</strong> (<em>array-like object</em>) – The a2 shifting vector.  If box is given, a2vect is taken as a
crystal lattice vector, otherwise as a Cartesian vector.</p></li>
<li><p><strong>a1</strong> (<em>array-like object</em>) – List of fractional coordinates along a1vect corresponding to the
E_gsf (and delta) values.</p></li>
<li><p><strong>a2</strong> (<em>array-like object</em>) – List of fractional coordinates along a2vect corresponding to the
E_gsf (and delta) values.</p></li>
<li><p><strong>E_gsf</strong> (<em>array-like object</em>) – List of generalized stacking fault energies for the positions
associated with the corresponding (a1, a2) fractional coordinates.</p></li>
<li><p><strong>box</strong> (<a class="reference internal" href="atomman.Box.html#atomman.Box" title="atomman.Box"><em>atomman.Box</em></a><em>, </em><em>optional</em>) – Defines unit cell box dimensions for conversion between crystal
lattice and Cartesian vectors.  If not given, will be set as a
square unit box, thus no conversion will occur (i.e. a1vect,
a2vect will be Cartesian).</p></li>
<li><p><strong>delta</strong> (<em>array-like object</em><em>, </em><em>optional</em>) – List of change in displacements normal to the fault plane for the
positions associated with the corresponding (a1, a2) fractional
coordinates.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.GammaSurface.xy_to_a12">
<code class="sig-name descname">xy_to_a12</code><span class="sig-paren">(</span><em class="sig-param">x</em>, <em class="sig-param">y</em>, <em class="sig-param">a1vect=None</em>, <em class="sig-param">a2vect=None</em>, <em class="sig-param">xvect=None</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.defect.GammaSurface.xy_to_a12" title="Permalink to this definition">¶</a></dt>
<dd><p>Conversion function from plotting x, y coordinates to normalized a1, a2
coordinates.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>x</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>(</em><em>s</em><em>)</em>) – Plotting x coordinate(s).</p></li>
<li><p><strong>y</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>(</em><em>s</em><em>)</em>) – Plotting y coordinate(s).</p></li>
<li><p><strong>a1vect</strong> (<em>np.array</em><em>, </em><em>optional</em>) – Crystal vector for the a1 vector.  Default value of None uses the
saved a1vect.</p></li>
<li><p><strong>a2vect</strong> (<em>np.array</em><em>, </em><em>optional</em>) – Crystal vector for the a2 vector.  Default value of None uses the
saved a2vect.</p></li>
<li><p><strong>xvect</strong> (<em>np.array</em><em>, </em><em>optional</em>) – Cartesian vector corresponding to the plotting x-axis. If None
(default), this is taken as the Cartesian of a1vect.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><ul class="simple">
<li><p><strong>a1</strong> (<em>float(s)</em>) – Fractional distance(s) along a1 vector.</p></li>
<li><p><strong>a2</strong> (<em>float(s)</em>) – Fractional distance(s) along a2 vector.</p></li>
</ul>
</p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.GammaSurface.xy_to_pos">
<code class="sig-name descname">xy_to_pos</code><span class="sig-paren">(</span><em class="sig-param">x</em>, <em class="sig-param">y</em>, <em class="sig-param">xvect=None</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.defect.GammaSurface.xy_to_pos" title="Permalink to this definition">¶</a></dt>
<dd><p>Conversion function from plotting x, y coordinates to Cartesian
positions.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>x</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>(</em><em>s</em><em>)</em>) – Plotting x coordinate(s).</p></li>
<li><p><strong>y</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>(</em><em>s</em><em>)</em>) – Plotting y coordinate(s).</p></li>
<li><p><strong>xvect</strong> (<em>np.array</em><em>, </em><em>optional</em>) – Cartesian vector corresponding to the plotting x-axis. If None
(default), this is taken as the Cartesian of a1vect.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><strong>pos</strong> – 3D Cartesian position vector(s).</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>np.array</p>
</dd>
</dl>
</dd></dl>

</dd></dl>

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